Trial transcript: Day 10 (October 17), PM Session, Part 1

Q. Thank you, Your Honor. Dr. Behe, I want to ask
you some questions about the term theory and its understanding in
the science community. As the record has shown so far that the
statement that is read to the students in this case uses this
definition, " A theory is defined as a well tested explanation
that unifies a broad range of observations." Is that a good
definition of a theory?

Q. Let me see if this is what your understanding
of that definition is. In science "a well substantiated
explanation of some aspect of the natural world that can
incorporate facts, laws, inferences, and tested hypotheses." Do
you agree with that definition?

A. Well, that's certainly one definition of the
word theory, but you have to be sensitive to the fact that the
word theory can be used in other senses as well.

Q. Now, using the National Academy of Sciences'
definition of theory, does that mean a theory is almost certainly
right?

A. No, it's not. And that might surprise some
people unless you, until you start to think of a couple of
examples, and perhaps I'd like to discuss two examples of a well
substantiated theory that was widely held, but nonetheless which
turned out to be incorrect. The first --

A. I did, but first let me mention something else.
Before -- let me ask, let me mention an older example that most
people are familiar with, and that's the example of geocentrism,
the idea that the earth is the center of the solar system, the
center of the universe, and that the stars and sun circle around
the earth. Now, it turns out that was very well substantiated
because people could look up and watch the stars and the sun
circle around the earth.

So they had very good evidence to support their
view. Furthermore, that theory was used for ages to help sailors
and so on navigate the seas. So it was pretty well substantiated.
Nonetheless, of course as everybody knows it turned out to be
incorrect, and Copernicus proposed that in fact the sun is the
center of the solar system and that the earth, while revolving on
its axis, travels around the sun. So again that's an old example,
but nonetheless it shows that a well accepted theory nonetheless
is not necessarily correct.

A. Yes, a more modern example from the late 19th
century is something called the ether theory of the proposition
of light, and that's shown on this slide here. I pulled off an
article from the web describing ether theory from the
Encyclopedia Britannica, and they say that, "The ether theory in
physics, ether is a theoretical universal substance believed
during the 19th century to act as the medium for transmission of
electromagnetic waves, much as sound waves are traveled
elastically such as air. "The ether was assumed to be weightless,
transparent, frictionless, undetectable chemically or physically,
and literally permeating all matter and space."

Now, this theory arose from the fact that it was
known that light was a wave, and like waves in the ocean and
waves in air that we perceive as sound, waves need a medium to
travel in. But if light is a wave, what does it travel in in
space? Ether. Ether was the medium through which light
traveled.

A. Well, it's a good thing we use this article
from the Encyclopedia Britannica, because on the next slide we
see that a man named James Clerk Maxwell, who was arguably the
greatest physicist of the 19th century, wrote an article for the
Ninth Edition of Encyclopedia Britannica in the 1870's, the title
of which was Ether. And you should keep in mind when he wrote
this for this publication, this was not going to be read not only
by the general public at large, but by all physicists as
well.

So he was writing of the idea as it was commonly
held at that time in the highest levels of physics, and he wrote
the following: "Whatever difficulties we may have in forming a
consistent idea of the constitution of the ether, there can be no
doubt that the interplanetary and interstellar spaces are not
empty, but are occupied by a material substance or body which is
certainly the largest and probably the most uniform body of which
we have any knowledge."

Now, later on Einstein's work caused physics to
abandon the ether theory. Physicists no longer believed that the
ether does in fact fill space, but let's look further on the next
slide. This is a copy of James Clerk Maxwell's article taken from
a collection of his papers, his article on the ether, and I want
to concentrate on the lower portion down here and I think on the
next slide that's blown up a little bit.

I'm not going to read this, I'm just going to
point out that you can observe that he's using a lot of precise
numbers about the energy of light by the sun, and it turns out
he's using that to do calculations, and in the calculations he is
deducing the properties of the ether. For example, these large
red arrows are pointing to the coefficient of rigidity of ether,
which is given by the formula Ro V squared, which is 842.8.

The next red arrow points to a line labeled
density of ether, which is equal to Ro, which is equal to 9.36
times 10 to the minus 19th power. Now, the point I want to make
using this slide is that James Clerk Maxwell, the greatest
physicist of his time, whose equations for electricity and
magnetism are still ought to physics students today, was using
his well accepted theory to do precise calculations and deduce
precise physical properties of a substance that did not exist.
And so the point is that even a well accepted theory, even a
feature which seems to be required by something else such as the
wave nature of light, can nonetheless be inaccurate and turned
out to be not only wrong, but utterly imaginary.

Q. Again I guess that would demonstrate the nature
that scientific theories are tentative, is that correct?

A. Yes, I think that it helps to make that claim
that scientific theories are tentative more than just a
hypothetical claim. The history of science is replete with
examples of what seemed to be correct explanations which turned
out to be incorrect.

Q. Now, is Darwin's theory of evolution a theory
in the sense of the National Academy of Sciences' definition?

A slide here is an excerpt from a book written by
a man named Ernst Mayr, who, Ernst Mayr was a very prominent
evolutionary biologist, who died just I think last year at the
age of 100, and was privy to a lot of the development of what's
called neo-Darwinian theory in the middle of the 20th century,
and he wrote a book entitled One Long Argument, and in it he
makes the case that Darwin's theory is not some single entity,
and let me just quote from that.

He says, "In both scholarly and popular literature
one frequently finds references to Darwin's theory of evolution
as though it were a unitary entity. In reality, Darwin's theory
of evolution was a whole bundle of theories, and it is impossible
to discuss Darwin's evolutionary thought constructively if one
does not distinguish its various components. The current
literature can easily lead one perplexed over the disagreements
and outright contradictions among Darwin specialists, until one
realizes that to a large extent these differs of opinion are due
to a failure of some of these students of Darwin to appreciate
the complexity of his paradigm." So you have to realize that
Darwin's theory is not a single claim. There are multiple claims
within what's called Darwin's theory, and they can be, they can
have different levels of evidence behind them.

Q. Did he break out these five claims in this One
Long Argument that you're referring to?

A. Yes, he did. He went on to say, well what are
those ideas that are grouped together under Darwin's theory? He
called them, he identified five different components, the first
of which is "evolution as such." He says this is the theory that
the world is not constant or recently create nor perpetually
cycling, but rather is steadily changing. So what we might call
change over time.

Q. Is that a theory or is it an empirical
observation of facts? How would you describe that?

A. Well, yeah, I myself would call that more an
observation rather than a theory. We see that the earth seems to
have changed over time. The second --

A. The second aspect of Darwin's theory that Mayr
discerned was common descent. This is the theory that, "Every
group of organisms descended from a common ancestor and that all
groups of organisms, including animals, plants, and
microorganisms, go back to a single origin of life on earth." The
third point is something called multiplication of species. This
theory explains the origin of enormous organic diversity.

I won't read the rest of the quote there, but it's
just a question why are there so many species, the multiplication
of species. The fourth component of Darwin's theory according to
Mayr is something called gradualism. According to this theory,
"Evolutionary change takes place through the gradual change of
populations and not by the sudden saltational production of new
individuals that represent a new type." So gradualism, things
thing gradually over time.

And the last component according to Mayr is
natural selection. According to this theory, "Evolutionary change
comes through the abundant production of genetic variation, the
relatively few individuals who survive, owing to particularly
well adapted combinations of inheritable characters, give rise to
the next generation." So this is what's commonly called survival
of the fittest.

Q. Is this strength of the scientific evidence
equal for each of these five separate claims?

A. No, they vary greatly in the strength of
evidence that's behind each of those.

Q. Has it been your experience that supporters of
Darwin's theory of evolution and opponents of intelligent design
have conflated the evidence for the occurrence of evolution, the
change over time, with the evidence for the mechanism of
evolution, natural selection?

A. Yes. In my experience many people confuse the
various parts of Darwin's theory. They don't make the distinction
that Ernst Mayr makes, and people see that there has been change
in the world and a lot of people then assume that because there
has been change in the world, then it must have been change
driven by natural selection. And that's a mistaken
conclusion.

Q. Are there other senses in which the word theory
is used by scientists?

A. Yes. You have to realize that scientists
themselves use the word theory in a very broad, with a very broad
range of senses. Not only in the sense that the National Academy
gave to it, but scientists themselves use it to indicate many
other things.

Q. Now, you did a search of Pub Med searching for
the term theory, is that correct?

A. Yes, that's right. In order to illustrate how
scientists themselves use the word theory, I did a search in a
database called Pub Med, which is maintained by the National
Library of Medicine, which is a division of the National
Institutes of Health of the federal government, and this is a
database of abstracts and titles of almost all biological
articles that are published. It contains millions and millions of
articles.

A. Yes, I have. In this first one, which might be
a little bit hard for me to read, but nonetheless the red arrow
down here, I certainly won't read the whole abstract, but if you
can see the little red arrow down here, let me just read a phrase
from this. This says that, "This study does not support the
previous theory." And so they are using the word theory here to
mean a previous idea that has now been shown to be wrong or have
evidence against it.

Q. If I may, Dr. Behe, just interrupt you here
briefly that might help you in your testimony as well, if you go
to the exhibit book that you've been provided, and if you look
under Tab 8 I believe, there's an exhibit marked Defendant's
Exhibit 203-A, as in Alpha.

Q. And if it will help you to perhaps look at
those as opposed to trying to review it on the screen, work
between the two.

A. Okay. Thank you. And the next slide up on the
screen here is if you follow the red arrows, and those points to
other occasions of the word theory, it says in this article, "The
membrane pacemaker theory of aging is an extension of the
oxidative stress theory of aging." So in here the scientists are
using the word theory to explain, or to refer to ideas that are
very limited in scope, which may or may not have much evidence to
support them.

So in a much different sense than the National
Academy used in its booklet. You could go to -- oh, thank you for
the next slide. Let me just see if I can find that one article.
Here it is. Okay. If you look at this other article from Pub Med,
it's pointing to a sentence that begins, "In theory, change in
climate would be expected to cause changes elsewhere."

So again a scientist here is using the world
theory to refer to, you know, we would expect this to happen, a
kind of expectation. Now, I put up here a publication of my own
that I published with my dissertation advisor Walter Englander,
and if you could read the top it reads, "mixed gelation theory,"
and it refers to mixtures of sickle cell hemoglobin with other
types of hemoglobin. So again we were using the word theory to
describe ideas and results that have a very limited
providence.

And finally on the next slide this is an article
taken from an issue of Science Magazine seven years ago, a
special issue which focused on the question of why is there
sexual reproduction. And the article was entitled "Why Sex?
Putting Theory to the Test," and the author said the following.
"Biologists have come up with a profusion of theories since first
posing these questions a century ago." These questions meaning
why is there sexual reproduction, and again the author here is
using the word theory in terms of competing hypotheses, competing
ideas, none of which have much evidence behind it, none of which
have wide acceptance in the scientific community.

Q. I want to return to Ernst Mayr and ask you are
the parts of Darwin's theory as he's listed here well tested?

A. No, they are not. If you look at the top ones,
evolution as such, common descent, multiplication of species,
those are all well tested. The claim of gradualism is in my
opinion rather mixed. There's evidence for, and some people argue
against it. But the component of Darwin's theory natural
selection which is sometimes viewed as the mechanism that Darwin
proposed for evolution is very poorly tested and has very little
evidence to back it up.

Q. I want to go through in a little bit more
detail on some of these claims. Going back to that first claim,
and I believe you testified probably akin to an empirical
observation, is that correct?

A. Yes, evolution as such that the world is
changed over time, and life as well.

A. No, it certainly has no argument with this
component of Darwin's theory. As a matter of fact I think there
is a, on the next slide there's an excerpt from Of Pandas and
People where the authors write, "When the word is used in this
sense, that is the sense of change over time, it is hard to
disagree that evolution is a fact. The authors of this volume
certainly have no dispute with that notion. Pandas clearly
teaches that life has a history, and that the kinds of organisms
present on earth have changed over time." And let me make the
point that Ernst Mayr calls this component evolution as such.
That is the basic idea of evolution.

Q. So when you hear a claim that intelligent
design is anti-evolution, are those accurate?

A. Well, some people point to empirical
difficulties that they see for common descent, but common descent
itself is not a claim, either for or against is not a claim of
intelligent design theory.

Q. Would it be accurate then to say it's viewed
more as a difficulty with Darwinism rather than a claim for
intelligent design?

A. Yes, that's correct. Common descent applies
more to Darwinian claims, which claim descent with modification,
than it does to intelligent design, because intelligent design is
focused exclusively on the question of whether we can discern the
effects of intelligence in life.

Q. In which of these claims is intelligent design
focused principally upon?

A. Intelligent design focuses exclusively on the
fifth claim of Ernst Mayr, or the fifth component that Ernst Mayr
identified in Darwin's theory, that of natural selection, or in
other words what is the mechanism of evolution, how could such
things happen.

Q. Is it your view that that is where the
scientific evidence for these five claims is perhaps the
weakest?

A. Yes, that is in fact the most poorly supported
aspect of Darwin's theory. As a matter of fact, that's where the
evidence in my view points away from Darwin's theory.

Q. Again so does intelligent design question all
parts of Darwin's theory of evolution?

A. No. It focuses exclusively on the question of
the mechanism of evolution, and I tried to make that clear as
this picture shows. This is an issue of something called the
reports of the National Center for Science Education, which is a
group which strongly advocates for the teaching of Darwinian
evolution in school, and I wrote a letter to the editor of The
Reports, which was published in an issue approximately four years
ago.

And here's an excerpt from that letter where I
explain, "The core claim of intelligent design theory is quite
limited. It says nothing directly about how biological design was
produced, who the designer was, whether there has been common
descent, or other such questions. Those can be addressed
separately." It says, "Only that design can be empirically
detected in observable features of physical systems."

And I go on to say, "As an important corollary it
also predicts that mindless processes such as natural selection
or the self-organization scenarios favored by Shanks and Joplin
will not be demonstrated to be able to produce irreducible
systems of the complexity found in cells." So I tried to clearly
explain that the only focus of intelligent design is on the
mechanism of evolution, or the question of whether or not aspects
of life show the marks of intelligent design.

Q. And you said this was published in The Reports
by the National Center for Science Education?

Q. And Dr. Alters and Forrest are also associated
with this organization?

A. I think Dr. Forrest is and Dr. Miller is. I'm
not sure about Dr. Alters, and also Professor Pennock has a reply
in that same issue of The Reports.

Q. Now, Dr. Miller in his expert report that he's
provided in this case said that Darwin's theory actually has many
mechanisms. Do you agree with that?

A. No, I disagree, and here is a little copy of
Professor Miller's expert report, and he lists a number of
things, including genetic recombination, transposition,
horizontal gene transfer, gene duplication, sexual selection,
developmental mutation and so on, and he says that, "The relative
importance of these and other mechanisms of evolution, these
conflicts continue to motivate."

So he seems to be calling these mechanisms. He's
making a mistake here. Except for sexual selection, all the other
components listed in his report, gene transfer, transposition,
recombination, are simply ways that diversity is generated in
nature. But diversity has to be acted upon in Darwin's
understanding by natural selection. So natural selection is the
only mechanism of Darwinian evolution. The sexual selection that
he lists, that is a mechanism, but it's a subset of natural
selection where features have selected value due to the
consideration of their ability to allow an organism to attract
mates or otherwise reproduce.

A. Yes, they do. Here's an excerpt from an article
by a man named Jerry Coyne, who was writing in a magazine called
The New Republic. Now, Jerry Coyne is a professor of evolutionary
biology at the University of Chicago and a vocal opponent of
intelligent design, as the title of the article shows. He writes
an article entitled The Case Against Intelligent Design.

Nonetheless, he disputes what Professor Miller has
said, the idea that he had talked about, Jerry Coyne says the
following, "Since Darwin's theories have been expanded, and we
now know that some evolutionary change can be caused by forces
other than natural selection. For example, random and nonadaptive
changes in the frequencies of different genetic variance, the
genetic equivalent of coin tossing, have produced evolutionary
changes in DN A sequences," and here is an important point.

"Yet, selection is still the only known
evolutionary force that can produce the fit between organism and
environment, or between organism and organism, that makes nature
seem designed." So Professor Coyne was saying that well, there
can be random genetic changes in organisms, but the only
mechanism pertinent to the discussion of whether there is design
in nature or not is Darwin's idea of natural selection.

Q. Do any other scientist besides intelligent
design proponents question the ability of natural selection to
explain various aspects of life?

A. Yes, a number of scientists who are not design
proponents also question the ability of natural selection to
account for features of life, and one example is shown on this
slide, a man named Stewart Kauffman, who is a professor of
biology at the University of Toronto now, in wrote a book called
The Origins of Order: Self organization and Selection in
Evolution, and that was published by Oxford University Press, and
in the introduction to his book he wrote the following, "Darwin's
answer to the sources of the order we see all around us is
overwhelmingly an appeal to a single singular force: natural
selection. It is this single force view which I believe to be
inadequate, for it fails to notice, fails to stress, fails to
incorporate the possibility that simple and complex systems
exhibit order spontaneously." So in this quotation Professor
Kauffman is summarizing his view that the Darwinian mechanism of
natural selection is inadequate to explain some features of
biology.

A. Yes, he does. He also contributed an article to
the book Debating Design, to which I and others also contributed,
which was published by Cambridge University Press last year in
which he reiterates his views about self-organization and
complexity. He wrote in the underlying bold portion, "Much of the
order in organisms I believe is self organized and spontaneous.
Self-organization mingles with natural selection in barely
understood ways to yield the magnificence of our teeming
biosphere. We must therefore expand evolutionary theory." In
other words natural selection is not sufficient. We have to
expand evolutionary theory to include something else other than
natural selection if we want to explain what we see in
biology.

Q. Sir, you've already shown that the theory of
evolution does not consist of a single claim, and you testified
that proponents of the theory of evolution tend to conflate
evidence for one claim to support another claim, and also you
testified that opponents of ID, intelligent design, claim that
it's anti-evolution, and you showed a slide of Pandas which
refutes that particular claim. Now, when we say, when we use the
term Darwin's theory of evolution, what is the common
understanding for that?

A. Well, the common understanding is that natural
selection has driven all of the change in the world, we see in
the biological world.

Q. Now, the evolution as such, understanding that
life is changed over time, that was understood before Darwin's
time, is that correct?

A. Yes. People have been proposing such things for
I think a couple of hundred years before Darwin's day. Darwin's
distinctive contribution to this discussion was the proposal of
natural selection. It was he who had proposed what people
considered to be a completely unintelligent mechanism for the
production of the complexity of life.

Q. With that understanding, sir, is Darwin's
theory of evolution a fact?

Q. Is there one principal contention you have with
the explanatory power of the theory of evolution that's is
particularly relevant for intelligent design?

A. Yes, I think the major overwhelming problem
with Darwin's theory is what I summarized in my expert report. I
stated the following, "It is my scientific opinion that the
primary problem with Darwin's theory of evolution is the lack of
detailed, testable, rigorous explanations for the origin of new
complex biological features."

MR. ROTHSCHILD: Your Honor, objection, just to the
extent I just want to make sure that the expert report is not
coming into evidence. I don't object to the slide as long as
that's clear.

MR. MUISE: The report is not coming, Your Honor.
It's just for demonstrative purposes to demonstrate his
opinion.

A couple of examples are shown next. Here is an
excerpt from a book by a man named Franklin Harold, who's an
emeritus professor of chemistry at Colorado State University, and
four years ago he published a book entitled The Way of the Cell
with Oxford University Press, and he quote, "We must concede that
there are presently no detailed Darwinian accounts of the
evolution of any biochemical system, only a variety of wishful
speculations." So he also seems to share that view.

A. Yes. Dr. Miller himself wrote in his expert
statement, "Living cells are filled of course with complex
structures," and let's skip down to the underlying bold
statement, he continues, "One might pick nearly any cellular
structure, the ribosome for example, and claim correctly that its
origin has not been explained in detail by evolution." So again
everybody agrees that Darwinian theory has not given an
explanation of many, many features of life.

Q. With that in mind, sir, I have some specifics I
want to ask you. Has the theory of evolution, in particular
natural selection, explained the existence of the genetic
code?

Q. Does this cause you to question whether a
Darwinian framework is the right way to approach such
questions?

A. Yes, it does, because if Darwinian theory is so
fruitless at explaining the very foundation of life, the cell,
then that makes a person reasonably doubt whether it's, whether
some other explanation might be more fruitful.

Q. Sir, in your expert opinion is there a problem
with falsification of Darwin's theory?

A. Yes, there's a big problem with that.
Falsification is roughly the idea that there is some evidence
which would make somebody change his mind that a theory was right
or not right. In many instances Darwinian theory is extremely
difficult to falsify, and let me give one example. On the next
slide is shown a figure of vertebrate embryos taken from a
biochemistry textbook by Voet and Voet, and this is the
biochemistry textbook that is used widely in colleges and
universities across the United States.

The figure here is drawn after a figure that was
first drawn in the 19th century by a man named Ernst Haekel, who
was an embryologist and supporter of Darwin's theory. As you see
in the figure, the vertebrate embryos all begin by looking
virtually identical, very extremely similar, and yet in the
course of their development they develop into completely
different organisms.

A fish, reptile, bird, amphibian, human, and so
on. And Ernst Haeckel thought it was exactly in accord with what
Darwin expected.

And the reasoning is illustrated by a quotation on
the next slide from a book entitled Molecular Biology of the
Cell, which was written by Bruce Alberts, who I mentioned earlier
was president of the National Academy of Sciences. One of his
co-authors is James Watson, the Nobel laureate who with Francis
Crick won the prize for discovering the double helical shape of
DNA, and other illustrious authors. And in the textbook they
explain those embryological facts by saying the following, "Early
developmental stages of animals whose adult forms appear
radically different are often surprisingly similar.

"Such observations are not difficult to
understand. The early cells of an embryo are like cards at the
bottom of a house of cards.

A great deal depends on them, and even small
changes in their properties are likely to result in disaster." So
if I can summarize their reasoning here, the authors were saying
these extremely similar embryos are exactly what we expect,
because in vertebrates the basic body plan is being laid down in
the early generations. And if you upset the foundation of a
structure, that's likely to essentially destroy it.

So what we expect is for later stages of
development to be dissimilar, but the earlier stages to be very,
very similar. Nonetheless, it turns out that those drawings were
incorrect, and a number of years ago in the late 1990's the
journal Science ran a story about a study that had been done to
try to reproduce Haeckel's, results, and it turns out they could
not be reproduced. And the story was entitled Haeckel's Embryos:
Fraud Rediscovered, and if you look at the illustration in the
news story, on the bottom row one sees the drawings of embryos as
Haeckel produced them, and on the top row you see photographs of
embryos which were taken by a modern team of embryologists,
looking very, very much different.

And on the next slide are excerpts from the news
story. It was written, it says, "Generations of biology students
may have been misled by a famous set of drawings of embryos
published 123 years ago by Ernst Haeckel. 'The impression they
give that the embryos are exactly alike is wrong,' says Michael
Richardson, an embryologist at St. George's Hospital Medical
School in London," and he was the lead author of the study which
showed the incorrectness of Haeckel's results.

"Not only did Haeckel add or omit features, but he
also fudges the scale to exaggerate similarities." Now, here is
the point with respect to the topic of falsification. Since these
studies have appeared, no Darwinian biologist that I'm aware of
has decided that Darwinian biology is incorrect. But if a theory,
Darwin's theory, can live with one result, and its utter opposite
with virtually identical embryos and with significant variation
in the embryos, then it says nothing about that topic.

It doesn't predict anything. It will live with
whatever result experimental science comes up with, which means
that Darwin's theory has nothing significant to say about a major
feature of life, embryology, because if you think about it, if
one kind of organism is to give rise to another kind of organism
over time, then the embryological plan for building that first
organism has to change into the embryological plan to build the
second kind of organism, and yet how that could happen is a topic
that Darwin's theory of evolution does not address in the
least.

Q. Sir, if I could direct your attention to the
exhibit book, under Tab 16, Defendant's Exhibit 271?

Q. Does the bacterial flagellum in the Type 3
secretory system, and we're going to be talking about these in a
little bit greater detail later, but is there an analogy also
with regard to the falsifiability that you could --

A. Yes. As I'll discuss later, again Darwinian
theory can't decide whether the Type 3 secretory system might
have arisen from the flagellum, the flagellum from the secretory
system, whether both developed independently, or other pertinent
questions. So again the question of falsifiability, if it
doesn't, can't predict any of those, then it has nothing to say
about those features.

Q. Now, does Darwin's theory have difficulty
explaining what we see in nature regarding sexual
reproduction?

A. Yes, turns out that it does. It was realized
not long after Darwin published his theory, it was realized by a
man named August Weisman that Darwinian theory actually predicts
that most organisms should reproduce asexually because, one
reason is because Darwinian theory, one goal of an organism, goal
in the terms of a better evolutionary result, is to get more of
the organism's genes into the next generation. If an organism
reproduced asexually by clonal reproduction, the offspring would
contain all of the genes of the organism. But during sexual
reproduction, for each offspring reproduced the parent gets only
half of its genes into the next generation.

And this has been a conundrum that has been
unsolved in Darwinian theory for over a century, and during that
time scientists have not just been sitting around. They've been
trying very hard to come up with explanations for that, and as a
matter of fact they've come up with so many suggestions, so many
theories, that in 1999 a man named Kondrashov published an
article in the journal Heredity entitled Classification of
Hypotheses on the Advantage of Amphimixis, and for amphimixis
read sexual reproduction. There were so many competing ideas that
he had to classify them into groups to try to keep better track
of them, and he --

A. Yes, in 1993, about ten years ago. Let me just
read the first sentence here, "After more than a century of
debate, the major factors of the evolution of reproduction are
still obscure."

Q. If I could direct your attention again to your
exhibit book, Tab Number 9, and it's listed as Defendant's 270,
is that the article you're referring to?

A. Yes, that's the one. And if I could continue
the quote after the bolded text, he continues, "During the past
25 years, hypotheses have become so numerous and diverse that
their classification is a necessity. The time is probably right
for this. No fundamentally new hypothesis has appeared in the
last five years, and I would be surprised and delighted if some
important idea remain unpublished." So he was expressing his view
that an exhaustive look had been done and that we have not yet
come up with an answer.

Q. Do you have additional slides and articles to
demonstrate this point?

A. Yes, that's right. This was in 1993. In the
year 1998 Science, the journal Science issued a special issue
which focused on the evolution of sex, and in that the leadoff
article of a number of articles in that issue was the one
entitled Why Sex? Putting Theory to the Test. Now, notice the
word theory is not being used in the sense that the National
Academy gives to it.

And if you look at this little abstract which is,
or this little blurb up on the left-hand corner I think on the
next slide that's enlarged, it stated that, "After decades of
theorizing about the evolutionary advantages of sex, biologists
are at last beginning to test their ideas in the real world." So
let notice a couple of things about that.

Again they're using theory, theorizing, in a sense
like brainstorming. Furthermore, they say that this
brainstorming, this theorizing goes on ahead of the activity of
testing it. And furthermore that the testing can be put off
decades from when the theorizing takes place.

Q. If I could direct your attention again to the
exhibit book under Tab 10 and there's an exhibit listed,
Defendant's Exhibit Number 269, is that a copy, it looks like an
on-line version copy of the article that you're referring to?

A. Yes. There's an excerpt from this article which
is on the next I think -- oh, yes, I'm sorry. Yes, this is kind
of a repeat of one that I've done already, "Biologists have come
up with a profusion of theories since first posing these
questions a century ago." So clearly this is an idea that has
stumped science for a very long time. Another excerpt from the
article is shown on the next slide. The author writes, "How sex
began and why it thrived remains a mystery. Why did sex overtake
asexual reproduction?" I'm going to skip down here, and the
author continues, "Sex is a paradox in part because if nature
puts a premium on genetic fidelity, asexual reproduction should
come out ahead. All this shuffling is more likely to break up
combinations of good genes than to create them. Yet nature keeps
reshuffling the deck."

Q. And if I could just so the record is clear,
those last two quotes that you read from were from which
articles?

A. They were from the article Why Sex? Putting
Theory to the Test by Bernice Wuethrich.

A. Yes, I do. This is a quotation of a man named
George Williams. George Williams is a prominent evolutionary
biology at the State university of New York at Stonybrook, and he
wrote a book in the mid 1970's entitled Sex and Evolution, and a
part of that book was quoted in a book recently by Richard
Dawkins of Oxford University, and the quotation is this. "This
book," that is George Williams' book, "this book is written from
a conviction that the prevalence of sexual reproduction in higher
plants and animals is inconsistent with current evolutionary
theory. There is a kind of crisis at hand in evolutionary
biology," and Dawkins comments on this quotation on the next
slide.

Richard Dawkins, an evolutionary biologist at
Oxford University, Dawkins says, this is Dawkins speaking,
"Maynard Smith and Hamilton," which refers to two prominent
evolutionary biologists, "said similar things. It is to resolve
this crisis that all three Darwinian heroes along with others of
the rising generation, labored. I shall not attempt an account of
their efforts, and certainly I have no rival solution to offer
myself."

So the point is that this problem is still
unresolved, and yet this goes to the very heart of evolutionary
theory, or a theory of evolution that expects that most species
would reproduce asexually can be likened to a theory of gravity
that expects that most objects will fall up. And in either case a
reasonable person might wonder if the theory is missing some
large piece of the puzzle, and certainly I think as an educator
students should be apprised of facts like these.

A. I think I have a little excerpt from my expert
report in which I dealt with that question, and I said the
following, "The problem that the Origin of Life poses for
Darwin's theory is the following. If the beginning of life
required something extra, something in addition to the
unintelligent operation of natural processes that Darwin's theory
invokes, then it would be fair for a curious inquirer to wonder
if those other processes ended with the beginning of life, or if
they continued to operate throughout the history of life," and
I'll stop there, close quote. So the point is this. If we cannot
explain the origin of life by unintelligent processes, and if
intelligent processes were in fact involved with that, then we
might wonder did they continue throughout the history of life, or
did they stop at that point.

Q. Sir, do you have an additional slide to make
this point regarding the questions of the origins of life is left
unresolved?

A. Yes, I do. Just a couple. It's easy to find
scientists involved in a study of the origin of life who are very
willing to say that we have not a clue as to how life started,
and here's a convenient source, this was an interview by PBS with
a man named Andrew Knoll, who is an eminent professor of biology
at Harvard who studies the early development of life, and one of
the topics they wanted to speak with him over was, "Why it's so
devilishly difficult to figure out how life got started."

And on the next slide they put the question to
Andrew Knoll, they say, "How does life form?" And Professor Knoll
says, "The short answer is we don't really know how life
originated on this planet." And skip a bit, "We remain in
substantial ignorance." Next slide, they asked another question,
the interviewer asked, "Will we ever solve the problem of the
origin of life?"

And Knoll says, "I don't know. I imagine my
grandchildren will still be sitting around saying that it's a
great mystery." So that here's a person involved in studying the
origin of life who says quite frankly that we don't know what's
going on and he doesn't have any particular expectation that our
grandchildren will understand the origin of life.

Q. Sir, if I could direct your attention to the
exhibit book under Tab 12, Defendant's Exhibit Number 267, is
that the interview that you've just been testifying to?

Q. I'd like to direct your attention to what I
have put up on the screen here is an excerpt from a booklet
entitled Science and Creationism which was put out by the
National Academy of Sciences in 1999, and if you could please
read that quote?

A. Yes. The National Academy wrote, "For those who
are studying the origin of life, the question is no longer
whether life could have originated by chemical processes
involving nonbiological components. The question instead has
become which of many pathways might have been followed to produce
the first cell," and I'll stop there, close quote.

A. Yes. I find it very disturbing, because in that
statement you don't see any reference to the results of workers
in the field. You don't see any reference to the data of what
people have come up with. Instead, in this publication they focus
on the attitudes of the scientists involved, and while the
attitudes might be an interesting sociological phenomenon, they
do not go to the question of whether we can explain the origin of
life.

And furthermore, this booklet is written for
teachers and indirectly then for their students, and by advising
teachers or letting teachers or by saying this to teachers, it
seems to me the National Academy is encouraging them to have
their students think of this problem in the same way that workers
have been doing for the past fifty years in the same way that has
proved fruitless for over half a century.

Q. Sir, is there a scientific controversy
regarding intelligent design in evolution?

A. Well, in addition to, you know, the articles
and counterarticles and things that have been mentioned earlier
in the day, and besides the conferences and symposia that I have
attended, there have also been a number of published books and
articles debating design, and a good example of that is shown on
the screen here, this is the cover of the book entitled, excuse
me, Debating Design: From Darwin to DN A ,and it was edited by
two people, William Dembski, who's a philosopher and
mathematician and intelligent design proponent, and Michael Ruse,
who's a professor of the philosophy of science and a student of
Darwinian thought, and in this number of academics contributed
chapters arguing not only about intelligent design and Darwinism,
but also complexity theory, self-organization, and other views as
well.

Q. And I believe you testified previously that
some of the experts that are testifying on behalf of plaintiffs
in this case have also contributed chapters to this particular
book?

A. That's correct. Kenneth Miller has a chapter in
there. I think Robert Pennock has a chapter in there as well.

Q. And I believe you also testified during the
qualifications portions that you contributed a chapter to a book
that was written by Robert Pennock, scientists debating the
question of intelligent design?

MR. ROTHSCHILD: He called it scientists debating
intelligent design, or something to that effect. He used the word
scientists. It's actually Intelligent Design and Its Critics, if
it's the Pennock edited book.

MR. MUISE: Okay. I don't see much a distinction
with that, Your Honor, but --

A. As its title implies, it was trying to group,
put into groups possible pathways that a Darwinian evolutionary
pathway might take, and it was particularly concerned with the
problem of irreducible complexity.

Q. Now, you testified that the design arguments
speaks of the purposeful arrangement of parts. Are there any
other aspects of the design argument?

A. Yes, and that's correct. There are other
aspects, and they're shown on the next slide. Just like Ernst
Mayr showed that there were several aspects to Darwinian theory,
there are aspects to the intelligent design argument. The
intelligent design argument itself, the positive argument for it
is the purposeful arrangement of parts, as I have described.

However, in an inductive argument, if somebody
else offers a counterexample to the induction, then one has to
address that to make the inductive argument stand. So there's
also a negative argument which says that despite Darwinian claims
that the inductive positive argument is unrefuted, that is that
Darwinism cannot account for the purposeful arrangement of
parts.

Q. So that's your argument against the
plausibility of a Darwinian explanation for design, is that
correct?

A. Yes. Now, what would make Darwinian
explanations seem implausible? Well, Charles Darwin himself wrote
how his argument could be refuted. In his writings in his book On
the Origin of Species he wrote that, "If it could be demonstrated
that any complex organ existed which could not possibly have been
formed by numerous successive slight modifications, my theory
would absolutely break down," adding, "but I can find out no such
case."

In this passage Darwin was emphasizing that his
was a gradual theory. Natural selection had to improve things
slowly, in tiny steps over long periods of time. If it seemed
that things were improving rapidly, in big leaps, then it would
start to look suspiciously as if random mutation and natural
selection were not the cause.

Q. Have other scientists acknowledged that this is
an argument against Darwin's theory of evolution?

A. Yes. In his book Finding Darwin's God Kenneth
Miller has written that, "If Darwinism cannot explain the
interlocking complexity of biochemistry, then it is doomed."

A. Yes. Richard Dawkins in his recent book The
Ancestor's Tail, from which I quoted recently, wrote "That it is
perfectly legitimate to propose the argument from irreducible
complexity, which is a phrase I use, as a possible explanation
for the lack of something that doesn't exist, as I did, for the
absence of wheeled mammals." Let me take a second to explain
Dawkins' reference.

He's saying that this problem is a problem for
biology, but nonetheless he thinks that everything in biology has
a Darwinian explanation. So that whatever we do see in biology
necessarily is not irreducibly complex, and I think in my opinion
that's an example of begging the question. But he does recognize
the concept of irreducible complexity.

Q. Sir, I'd like at this point for you to define
irreducible complexity, and we have a slide here.

A. Yes, in my article from the journal Biology and
Philosophy, I defined it this way. "By irreducibly complex, I
mean a single system which is necessarily composed of several
well matched interacting parts that contribute to the basic
function, and where the removal of any one of the parts causes
the system to effectively cease functioning."

Q. Now, you have up there "necessarily" in
italics. Is there a reason for that?

A. Yes, the definition that I gave in Darwin's
Black Box did not have those italicized words necessarily, but
after the books came out and an evolutionary biologists at the
University of Rochester named Allen Orr pointed out that it may
be the case that if you had a system that was already
functioning, already doing some function, it's possible for a
part to come along and just assist the system in performing its
function, but after several changes perhaps it might change in
such a way that the extra part has now become necessary to the
function of the system but that could have been approached
gradually.

And I, in thinking about it I saw that he was
thinking of examples that I did not have in mind when I wrote the
book. So I kind of tweaked the definition here in this article to
try to make it clear and try to exclude those examples that I
didn't have in mind.

Q. Is it a common practice within the science
community for a scientist to adjust, modify, or tweak their
theories based on criticisms that they get from other
scientists?

A. Oh, sure. That's done all the time. Nobody is
perfect, nobody can think of everything at once, and a person is
always grateful for criticism and feedback that helps to improve
an idea.

Q. Does criticism undermine the idea that you were
trying to convey by irreducible complexity?

A. No, it didn't. It clarified it, and after his,
after reading his SI I saw that he was thinking of things that I
did not have in mind. So I tried to clarify that.

Q. You have this system in underlying capitalized
and in red. What's the purpose for that?

A. Well, that to me has turned into a point of
confusion because some people, including Professor Miller, have
been focusing the discussion on the parts of the system and
saying if one removes a part and then can use the part for some
other purpose, then they say that means that it's not irreducibly
complex, but that is not the definition I gave to irreducible
complexity, that is not the concept of irreducible complexity
that I described in Darwin's Black Box. I said that if you take
away one of the parts from the system, the system, the function
of the system itself ceases to work, and whether one can use the
part for anything else is beside the point.

Q. So then it is fair to say Dr. Miller's uses the
wrong definition of your concept and then argues against that
different definition to claim that your concept is incorrect?

Q. Now, Dr. Padian testified on Friday that the
concept of irreducible complexity applies above the molecular
level, is that correct?

A. No, that is incorrect. In Darwin's Black Box I
was at pains to say that the concept of irreducible complexity
applies only to systems where we can enumerate the parts, where
we can see all the parts and how they work, and I said that in
biology therefore that necessarily means systems smaller than a
cell, systems whose active molecular components we can
elucidate.

When you go beyond a cell, then you're necessarily
talking about a system, an organ or animal or any such thing,
that is so complex we don't really know what we're dealing with,
and so it remains a black box, and so the term irreducible
complexity is confined to molecular examples.

Q. Well, I want to read to you several sections,
passages from Pandas that Dr. Padian referred to as claiming that
this is the concept of irreducible complexity, and I'd like your
comment on each one of those as I go through. The first one,
"Multifunctional adaptations where a single structure or trait
achieves two or more functions at once is taken as evidence by
the proponents of intelligent design of their theory," and the
reference is page 72 of Pandas.

Q. The question is, is that a definition or is
that within your concept of irreducible complexity?

A. No, that's not the way I define the term, and
I'm not quite sure what he has in mind.

Q. And the second example is, "Proponents of
intelligent design maintain that only a consummate engineer could
anticipate so effectively the total engineering requirements of
an organism like the giraffe." That's a citation from page 71. Is
that a reference to the concept of irreducible complexity?

A. No, it isn't. Again, irreducible complexity
focuses on the cell and systems smaller, because we have to
elucidate all the parts, and you have to keep in mind that the
parts of a biological system are molecular parts, even though
most people commonly think of large organisms. Let me just say
that, you know, that you should keep in mind that Darwinism has
other problems beyond irreducible complexity. So Pandas might
have been pointing to those.

Q. Two more such examples. The third one, two more
of out of four, this is the third out of four, "But it has not
been demonstrated that mutations are able to produce the highly
coordinated parts of novel structures needed again and again by
macroevolution." And again, is that referring to the concept of
irreducible complexity?

A. Well, again unless he's referring to the
molecular level, then no, that is not correct. It turned out that
molecular changes, small changes in DN A can actually cause large
changes in an organ. You might lose the finger or get a duplicate
of a finger or some such thing, so you have to apply the concept
of irreducible complexity to the molecular revel.

Q. And the last example, "Design theory suggest
that various forms of life began with their distinctive features
already intact, fish with fins and scales, birds with feathers,
beaks, and wings," that's a reference to page 25 of Pandas. Is
that a reference to the concept of irreducible complexity?

A. No, it is not. Again one more time, the concept
of irreducible complexity applies to the molecular level simply
because in biology the molecular level is where changes are
taking place. There are active components. That's where the
rubber meets the road in biology. So one has to restrict one's
self to that level.

Q. Is that the level where we can identify the
components of the systems?

A. Yes, that's the critical thing. We have to see
how things are working so we can realize what's going on and
decide whether or not an explanation is plausible.

Q. So it would be fair to say those four examples
I read to you may illustrate or highlight other difficulties with
Darwin's theory, but they're not specifically addressed in the
concept of irreducible complexity?

A. Yes, that's right. Just because irreducible
complexity is a problem, that doesn't mean that it's the only
problem.

Q. Now, again can you give us an example of an
irreducibly complex biochemical system?

A. Yes, an excellent example is again the
bacterial flagellum, which uses a large number of parts in order
to function, and again if you remove the components, if you
remove the propeller, if you remove the hook region, if you
remove the drive shaft or any multiple parts of the flagellum, it
does not work. It's ceases to function as a propulsive
device.

Q. Now, Professor Miller has testified that the
flagellum is not irreducibly complex. Do you agree with him?

Q. I'd like for you to go through and explain your
objections to his claim.

A. Okay. This is a slide from Professor Miller's
presentation on the flagellum. Let me just first read through the
slide completely and then I want to point to several
mischaracterizations that are contained on the slide. He writes,
"The observation that there are as yet no detailed evolutionary
explanations for certain structures in the cell, while correct,
is not a strong argument for special creation, 'design.' As
Michael Behe has made clear, the biochemical argument from design
depends upon a much bolder claim, namely that the evolution of
complex biochemical structures cannot be explained even in
principle."

This has three mischaracterizations I'd like to
point out in turn. The first one is what many people considered
to be an informal logical fallacy, and that is called poisoning
the well. It is given the reader a, leading the reader to suspect
the other person's argument. It's kind of a version of an ad
hominem argument. When he uses the term special creation and
quotation in design, that looks to me like he's indicating to the
reader that the people who make these arguments are trying to
mislead you into thinking that this is design, but it's really
special creation.

What's more, again the word creation has very
negative overtones and is used as a pejorative in many academic
and scientific circles. Furthermore, the phrase special creation
occurs nowhere in Darwin's Black Box. I never used the phrase
special creation in any of my writings except perhaps to say that
intelligent design does not require this. And so again I think it
is a mischaracterization and it appears to me an attempt to kind
of prejudice the reader against this, against my argument.

The second point is this. The second
mischaracterization is this. He says, "The observation that there
are as yet no detailed evolutionary explanations for certain
structures in the cell, while correct, is not a strong argument
for special creation that is 'design.'" Here Professor Miller is
doing something more understandable. He's essentially is viewing
my theory through the lens of his own theory. So all he sees is
essentially how it conflicts with his own theory and thinks that
that's all there is to it.

But as I have explained throughout the day today,
if we could go to the next slide, that an inability to explain
something is not the argument for design. The argument for design
is when we perceive the purposeful arrangement of parts, the
purposeful arrangement of parts such as we see in the flagellum,
such as we see the molecular machinery such as described in that
special issue of Cell and so on.

We can go to the next slide, this is a copy of the
first slide of Professor Miller's, the third mischaracterization
is this. He says, "As Michael Behe has made clear, the
biochemical argument from design depends upon a much bolder
claim, namely that the evolution of complex biochemical
structures cannot be explained even in principle." This is a
mischaracterization. It's essentially absolutizing my argument.
It's making overstating my argument in order to make it seem
brittle, to make it more easily argued against.

A. Yes, if you read Darwin's Black Box you see
that I say the following, "Even if a system is irreducibly
complex and could not have been produced directly, however one
cannot definitely rule out the possibility of an indirect
circuitous route. As the complexity of an interacting system
increases though, the likelihood of such an indirect route drops
precipitously."

So here I was arguing well, there's a big problem
for Darwinian theory. These things can't be produced directly,
but nonetheless you can't rule out an indirect route, but
nonetheless building a structure by changing its mechanism and
changing its components multiple times is very implausible and
the likelihood of such a thing, the more complex it gets, the
less likely it appears. So the point is that I was careful in my
book to qualify my argument at numerous points, and Professor
Miller ignores those qualifications.

Q. Do these qualification also demonstrate the
tentative nature in which you hold your theories?

A. Yes, that's right. I always -- well, I try to
state it in what I thought was a reasonable way and in a
tentative way as well.

Q. I believe we have a couple of more slides from
Dr. Miller that you --

A. Yes, this is essentially a continuation. These
will be slides number 2 and 3 from his slides on the flagellum.
This is just a continuation of his overstated arguments. He says,
"The reason that Darwinian evolution can't do this is because the
flagellum is irreducibly complex," and he quotes my definition of
irreducible complexity from Darwin's Black Box, and continue on
the next slide.

And he states that, "That claim is the basis of
the biochemical argument for design." But again that is not the
basis for the biochemical argument for design. The basis for the
biochemical argument for design is the purposeful arrangement of
parts. Irreducible complexity shows the difficulties for
Darwinian processes in trying to explain these things.

Q. Now, Dr. Miller claims that natural selection
can explain the flagellum. Do you agree with that claim?

Q. Dr. Miller claims that natural selection can
explain the bacterial flagellum. Do you agree with that
claim?

A. No, I disagree, and we go on to the next slide,
which is another one of Professor Miller's slides from his
presentation on the bacterial flagellum, and he tried to explain
molecular machines using kind of simple concepts to try and make
it more understandable to a broad audience. So for example on the
right-hand side which he labels "Evolution," he has little
colored hexagons, which are exist, which are separated, and then
he has the hexagons forming little groups and arrows pointing
between the hexagons and the groups of hexagons, and finally
there is kind of a large aggregation of hexagons.

On this, which he labels "Design," he has the
colored hexagons separate and arrows pointing to a larger
aggregation of hexagons. Now, I'm sure Professor Miller was
trying to get across a concept which is difficult, but in my
viewing and my understanding and presenting it this way, this
overlooks enormous problems that actual molecules would encounter
in the cell.

Q. Have you addressed these claims in other
writings that you have done?

A. Yes. Professor Miller has presented exactly the
same argument in several other settings, and I have addressed it
several times, most recently in my chapter in Debating Design,
and if you go to the next slide --

A. Yes, this is Figure 2 from that chapter. And
the slide is entitled "An irreducibly complex molecular machine,
can it arise from individual functional precursors." I used
little colored squares instead of hexagons, but nonetheless the
concept is kind of the same. The colored squares are supposed to
represent individual proteins which perhaps existed in the cell
already, there is six different ones, and the complex molecular
machine now is supposed to be an aggregate of all six proteins
with a new function that the system has that the individual parts
did not have. Unfortunately while this illustrates, you know,
something, it leaves out many concepts which are critical to
evaluating the likelihood of such a thing. May I continue?

A. For example, proteins, the components of
molecular machines are not little colored squares. They are not
little colored hexagons. They are very complex entities which we
will see in a second. Additionally, notice this red square. The
red square with the little arrow places it against the green
square and the yellow and the blue. Why is it there? Why didn't
it go down there? Why is it sticking to B and C and D? Why
doesn't it float away?

None of those questions are answered, this is an
oversimplified way to look at a very complex problem. For
example, let me just make one more comment. Notice that in
machines in our common experience, if you put a part in a place
different from where it usually is, that often times breaks the
machine. If in an outboard motor you took the propeller and you
put it on top instead of down by the rotor, then the machine
would not function. And it's the exact same way for molecular
machines.

Q. Have you prepared some slides to demonstrate
some of the more complexity of these parts?

A. Yes, I'm afraid we're going to have to go a
little bit into the complexity of these molecular systems.